PDB-6n91: Crystal Structure of Adenosine Deaminase from Vibrio cholerae Com...

ID or keywords:

Entry

Database: PDB / ID: 6n91

Title

Crystal Structure of Adenosine Deaminase from Vibrio cholerae Complexed with Pentostatin (Deoxycoformycin)

Components

Adenosine deaminase

Keywords

HYDROLASE / deaminase / pentostatin / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

inosine biosynthetic process / adenosine deaminase / adenosine catabolic process / adenosine deaminase activity / hypoxanthine salvage / purine ribonucleoside monophosphate biosynthetic process / nucleotide metabolic process / nucleobase-containing compound metabolic process / zinc ion binding / cytosol
Similarity search - Function

Biological species

Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Maltseva, N. / Kim, Y. / Endres, M. / Welk, L. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: Crystal Structure of Adenosine Deaminase from Vibrio cholerae Complexed with Pentostatin (Deoxycoformycin) (CASP target)
Authors: Maltseva, N. / Kim, Y. / Endres, M. / Welk, L. / Joachimiak, A.

History

Deposition	Nov 30, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 19, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6n91.cif.gz	298.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6n91.ent.gz	243.5 KB	Display	PDB format
PDBx/mmJSON format	6n91.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6n91_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	6n91_full_validation.pdf.gz	1.2 MB	Display
Data in XML	6n91_validation.xml.gz	30 KB	Display
Data in CIF	6n91_validation.cif.gz	43.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n9/6n91 ftp://data.pdbj.org/pub/pdb/validation_reports/n9/6n91	HTTPS FTP

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Related structure data

Related structure data	6n9mS S: Starting model for refinement
Similar structure data	2fcu-d 1q7q-1 5jd5-6 3amc-d 4c87-1 6uob-d 4c89-1 4ofc-3 1q8a-1 4ob8-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: IDP04388

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #158 - Feb 2013 Proton-Gated Urea Channel similarity (1)

Deposited unit

A: Adenosine deaminase

B: Adenosine deaminase

hetero molecules

76.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	134.906, 134.906, 136.144
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

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Protein , 1 types, 2 molecules AB

#1: Protein	Adenosine deaminase / Adenosine aminohydrolase Mass: 37274.309 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria) Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: add, VC_2751 / Plasmid: pMCSG91 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: Q9KNI7, adenosine deaminase

#1: Protein

Adenosine deaminase / Adenosine aminohydrolase

Mass: 37274.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: add, VC_2751 / Plasmid: pMCSG91 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: Q9KNI7, adenosine deaminase

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Non-polymers , 10 types, 401 molecules

#2: Chemical	ChemComp-DCF / 2'-DEOXYCOFORMYCIN Mass: 268.269 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₁₆N₄O₄ / Comment: anticancer*YM
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID Mass: 221.317 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₉H₁₉NO₃S / Comment: pH buffer*YM
#5: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH₂O₂
#6: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#7: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#8: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#9: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#10: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#11: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 4.8 Å³/Da / Density % sol: 74.36 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 1.2M NaH2PO4/0.8M K2HPO4; 0.1M CAPS pH 10.5; 0.2M Li2SO4 PH range: 10.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97895 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2018
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97895 Å / Relative weight: 1
Reflection	Resolution: 2.05→50 Å / Num. obs: 89846 / % possible obs: 100 % / Redundancy: 7.9 % / B_iso Wilson estimate: 37.16 Å² / R_merge(I) obs: 0.146 / Net I/σ(I): 19.1
Reflection shell	Resolution: 2.05→2.09 Å / Redundancy: 7.5 % / R_merge(I) obs: 0.967 / Mean I/σ(I) obs: 2.18 / Num. unique obs: 4470 / CC_1/2: 0.773 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	1.12_2829	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6N9M

6n9m

Resolution: 2.05→47.914 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 16.69

	R_factor	Num. reflection	% reflection
R_free	0.1744	4409	4.92 %
R_work	0.1538	-	-
obs	0.1549	89667	99.75 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.05→47.914 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5120	0	120	385	5625

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	5737
X-RAY DIFFRACTION	f_angle_d	0.991	7842
X-RAY DIFFRACTION	f_dihedral_angle_d	18.403	3490
X-RAY DIFFRACTION	f_chiral_restr	0.057	899
X-RAY DIFFRACTION	f_plane_restr	0.005	1036

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.0502-2.0735	0.2589	133	0.2217	2774	X-RAY DIFFRACTION	98
2.0735-2.0979	0.26	138	0.2137	2772	X-RAY DIFFRACTION	98
2.0979-2.1235	0.2298	173	0.2028	2766	X-RAY DIFFRACTION	99
2.1235-2.1503	0.2153	115	0.1819	2817	X-RAY DIFFRACTION	100
2.1503-2.1786	0.1737	179	0.1817	2839	X-RAY DIFFRACTION	100
2.1786-2.2085	0.1928	139	0.1773	2795	X-RAY DIFFRACTION	100
2.2085-2.24	0.2176	151	0.1717	2800	X-RAY DIFFRACTION	100
2.24-2.2735	0.1876	121	0.174	2881	X-RAY DIFFRACTION	100
2.2735-2.309	0.1959	146	0.1624	2815	X-RAY DIFFRACTION	100
2.309-2.3468	0.1986	150	0.1683	2798	X-RAY DIFFRACTION	100
2.3468-2.3873	0.2132	167	0.1633	2830	X-RAY DIFFRACTION	100
2.3873-2.4307	0.1846	125	0.1638	2851	X-RAY DIFFRACTION	100
2.4307-2.4775	0.194	129	0.165	2826	X-RAY DIFFRACTION	100
2.4775-2.528	0.1902	122	0.1704	2874	X-RAY DIFFRACTION	100
2.528-2.583	0.2112	160	0.1756	2797	X-RAY DIFFRACTION	100
2.583-2.6431	0.2203	127	0.181	2849	X-RAY DIFFRACTION	100
2.6431-2.7092	0.256	154	0.1812	2836	X-RAY DIFFRACTION	100
2.7092-2.7824	0.2207	134	0.1836	2860	X-RAY DIFFRACTION	100
2.7824-2.8643	0.2114	131	0.1788	2852	X-RAY DIFFRACTION	100
2.8643-2.9567	0.1877	165	0.1825	2817	X-RAY DIFFRACTION	100
2.9567-3.0624	0.2354	117	0.1811	2883	X-RAY DIFFRACTION	100
3.0624-3.185	0.1954	175	0.1769	2827	X-RAY DIFFRACTION	100
3.185-3.3299	0.2082	158	0.1748	2827	X-RAY DIFFRACTION	100
3.3299-3.5054	0.1741	184	0.1575	2822	X-RAY DIFFRACTION	100
3.5054-3.7249	0.1497	168	0.1456	2836	X-RAY DIFFRACTION	100
3.7249-4.0124	0.1479	129	0.1259	2895	X-RAY DIFFRACTION	100
4.0124-4.416	0.1328	132	0.1105	2896	X-RAY DIFFRACTION	100
4.416-5.0543	0.1221	132	0.1136	2934	X-RAY DIFFRACTION	100
5.0543-6.3656	0.1527	177	0.1342	2890	X-RAY DIFFRACTION	100
6.3656-47.9269	0.144	178	0.1479	2999	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	5.5364	-5.1269	1.9137	7.7958	-1.876	2.7478	0.1542	0.08	-0.0932	-0.1612	-0.1187	-0.4693	0.1774	0.4449	-0.0028	0.2135	0.0341	-0.0131	0.4271	-0.0164	0.3713	103.2393	-59.3034	34.9429
2	7.603	-1.597	-2.3658	1.3557	0.5488	3.4698	-0.1061	-0.2793	-0.5449	0.0277	0.1277	0.1908	0.4155	-0.0174	-0.0077	0.2974	-0.0482	-0.0453	0.1859	0.0141	0.2771	67.9254	-60.0302	11.8629
3	3.2708	-2.9572	0.9793	9.152	1.5942	7.7543	-0.3357	-0.2458	-0.05	0.538	0.5125	-0.4591	0.747	0.7513	-0.1719	0.228	0.0353	-0.0015	0.3611	-0.0056	0.2818	83.2378	-58.0309	17.6914
4	2.9031	0.0252	-0.602	2.6001	0.0899	2.4607	-0.0279	0.1394	-0.3976	-0.2471	-0.007	-0.1129	0.4472	0.0838	0.0226	0.3401	0.0231	-0.0185	0.2447	-0.0101	0.2715	72.9932	-58.1684	5.6254
5	2.0417	8.8485	-8.4147	2.0452	-8.4874	2.0313	-0.6982	0.9527	-0.7817	-1.2996	0.6865	-0.3323	1.5017	-0.5812	0.155	0.747	-0.0726	0.0702	0.4912	-0.0713	0.523	66.4674	-64.3666	-2.1717
6	3.2158	1.9898	-0.7954	5.2705	-1.16	2.7787	-0.0651	0.304	-0.0359	-0.4754	0.053	0.0638	0.1726	-0.1125	0.0093	0.2702	0.0201	-0.0163	0.2873	0.0067	0.2169	68.2074	-45.5164	-3.7032
7	1.6636	-0.1193	0.3758	2.2318	-0.8575	4.5822	-0.002	0.0163	0.1973	-0.0275	0.0702	0.2625	-0.1587	-0.3268	-0.0685	0.2119	0.0136	0.0022	0.2818	0.0196	0.3018	60.0767	-37.8081	8.7359
8	8.4371	-1.7271	2.4932	2.576	-0.433	3.6658	-0.1191	-0.3922	0.4803	0.2201	0.0823	0.0517	-0.1588	-0.2899	0.0776	0.2379	-0.0133	0.0596	0.2234	0.0288	0.1965	61.0723	-41.7956	19.7248
9	2.017	-7.8862	-4.0267	5.9981	3.1938	3.3336	-0.1628	-0.365	-0.2637	0.2036	0.0998	0.3221	0.2391	0.0054	0.0439	0.2895	-0.0492	0.0008	0.3694	-0.0108	0.3232	62.6512	-52.7906	22.6221
10	4.63	2.3226	2.9469	4.2613	2.7711	7.338	0.0447	-0.0445	-0.1792	0.0413	-0.0593	0.3868	0.3286	-0.7978	0.0263	0.1915	-0.0352	0.004	0.383	0.0343	0.3322	47.997	-53.6689	12.0602
11	8.5708	2.6515	-0.4288	2.4818	-0.2355	1.4425	-0.1616	0.3648	-0.2148	-0.158	0.1662	-0.0467	0.2802	0.162	0.0348	0.3397	0.0696	-0.0336	0.2896	0.0193	0.264	83.6628	-65.6012	31.0583
12	2.8141	0.9556	2.4363	4.8329	3.0216	5.7753	-0.0663	-0.053	-0.1323	-0.4405	0.1719	0.5803	-0.0224	-0.1081	-0.0808	0.2412	0.003	0.0006	0.28	0.0607	0.293	68.3754	-60.8648	27.4938
13	4.6976	-0.2934	-1.3023	3.0734	0.9135	3.1237	0.0184	0.0732	-0.5987	-0.022	-0.0862	0.1603	0.5049	-0.0411	0.0798	0.2854	0.0152	-0.0385	0.2342	0.0253	0.2465	77.0185	-68.2583	35.0729
14	6.1452	0.5843	-3.3356	1.3751	0.3956	3.7792	-0.1977	-0.2641	-0.7549	0.1376	0.0078	0.0513	0.7378	0.167	0.1542	0.3861	0.068	-0.0171	0.2758	0.0934	0.3516	82.5807	-71.5332	40.4918
15	4.0893	-0.8694	-1.348	2.7019	0.7814	3.765	-0.1823	-0.5351	-0.4035	0.4087	0.1527	0.0798	0.4399	0.0948	0.0152	0.2967	0.0363	-0.0048	0.3283	0.0801	0.2514	81.7779	-63.1474	50.1981
16	1.9245	0.8825	-0.8406	8.8063	-2.419	4.5438	0.0365	-0.4292	-0.0062	0.4862	-0.039	-0.1284	-0.0881	0.2186	-0.0338	0.2463	0.0526	-0.0227	0.4301	-0.0225	0.2637	87.5767	-51.9623	50.9623
17	4.8261	1.4295	2.192	3.9495	3.3605	6.5153	0.047	-0.1161	0.0486	0.1021	0.2858	-0.3994	-0.0163	0.7834	-0.2928	0.2107	0.0002	0.0355	0.3678	0.0076	0.3061	92.8919	-46.7139	42.93
18	6.7953	3.2245	1.1811	2.0904	1.0644	2.0321	0.0452	0.096	0.2715	0.0473	-0.0106	0.0319	-0.0463	0.061	-0.0558	0.2133	0.0453	0.0238	0.2387	0.0395	0.235	89.0646	-49.026	31.6562

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 302 through 334 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 1 through 30 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 31 through 55 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 56 through 111 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 112 through 130 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 131 through 189 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 190 through 251 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 252 through 279 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 280 through 301 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 302 through 334 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 1 through 30 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 31 through 55 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 56 through 89 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 90 through 130 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 131 through 180 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 181 through 228 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 229 through 251 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 252 through 301 )

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+About Yorodumi

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-Feb 9, 2022. New format data for meta-information of EMDB entries

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-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Open data

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Basic information

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Download

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Validation report

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Links

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Assembly

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Components

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Protein , 1 types, 2 molecules AB

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Non-polymers , 10 types, 401 molecules

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Experimental details

-
Experiment

-
Sample preparation

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Data collection

-
Processing

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About Yorodumi

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi